Recent research 1 carried out by Associate Professor Satchidananda Panda at Salk’s regulatory Biology Laboratory in California, has discovered that our gut microbiome differs in constitution dependent on the time of day. 
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Our gut bacteria have circadian rhythms too

The Study

Research was performed on mice, which showed that their gut flora followed distinct circadian rhythms, with some bacteria being found in higher concentrations at night or during periods of inactivity and fasting, and others being more prevalent during the daytime. During the clinical trial two groups of mice were fed either a normal diet, or a high fat diet. Those in the high fat diet were also encouraged to eat around the clock, therefore disrupting their usual sleep/wake pattern, whereas those on the ‘normal’ diet only ate during their regular waking hours.
 
It was found that the group following the ‘normal’ diet displayed large fluctuations in bacterial diversity throughout the 24 hour period, whereas those fed a high fat diet and with disrupted sleep patterns showed a marked reduction in these natural, circadian fluctuations. For example, levels of bacteria from the ‘firmicutes’ phyla tend to be higher during the daytime when we are eating, but should drop whilst we are sleeping. If, for some reason, this rhythm is disrupted levels of firmicutes stays constant throughout the day and night. This constant exposure to high concentrations of firmicutes is implicated in obesity. If you would like to read more about gut bacteria and its effect on weight management, check out the following link:

Blog post : Gut microbiota of slim people may help treat obesity.

What does this mean?
The research shows that it is not only what you eat, but also when you eat it that matters to the microbiome. Eating when the body should be sleeping, and is not programmed to be digesting appears to negatively impact on our gut flora.
woman working night shifts
Working night shifts affects our microbiome
Scientists have known for some time that both jet-lag and nocturnal shift working can cause health problems. It was previously thought that this was mainly through the disruption to normal hormonal patterns, however this latest research adds extra complexity. 

The fact that people with chronically disturbed day/night cycles due to frequent long haul flights or shift work have a tendency to develop obesity and other metabolic complications, is now known to be at least partly due to the loss of bacterial circadian rhythms, as well as the loss of the ‘hosts’ own circadian and hormonal rhythms.

Professor Panda’s group are still investigating the implications of these findings, and are yet to fully understand how and why our bacterial populations should change over a 24 hour cycle. 
But, it might be that helping your probiotic colonies to flourish through sensible food choices, and probiotic supplementation, could be even more important for those people who do a lot of international air travel, or for those who work night shifts, in order to normalise the microbiota.

Reference: 1. Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome." DOI: dx.doi.org/10.1016/j.cmet.2014.11.008

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